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AMINO ACIDS
- OVERVIEW
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The general structure of an amino acid
molecule, with the amine group on the
left and the carboxylic acid group on the
right. The R group is dependent on the
amino acid.
In chemistry, an amino acid is any
molucule that contains both amine and
carboxylic acid functional groups. In
biochemistry, this shorter and more
general term is frequently used to refer
to alpha amino acids: those amino acids
in which the amino and carboxylate
functionalities are attached to the same
carbon, the so-called α–carbon.
An amino acid residue is what is left of
an amino acid once a molecule of water
has been lost (an H+ from the
nitrogenous side and an OH- from the
carboxylic side) in the formation of a
peptide bond.
OVERVIEW cont.
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Amino acids are the basic structural building units
of proteins. They form short polymer chains called
peptides or polypeptides which in turn form
structures called proteins. The process of such
formation from an mRNA template is known as
translation, which is part of protein synthesis.
Phenylalanine is one of the standard amino acids.
OVERVIEW cont.
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Twenty amino acids are encoded by the standard
genetic code and are called proteinogenic or
standard amino acids. Combinations of these
amino acids produce every single essential
protein for the homeostasis of the human body. At
least two others are also coded by DNA in a nonstandard manner as follows:
Selenocysteine is incorporated into some proteins
at a UGA codon, which is normally a stop codon.
Pyrrolysine is used by some methanogens in
enzymes that they use to produce methane. It is
coded for similarly to selenocysteine but with the
codon UAG instead.
OVERVIEW cont.
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Other amino acids contained in proteins are
usually formed by post-translational modification,
which is modification after translation in protein
synthesis. These modifications are often essential
for the function of the protein.
Proline is the only proteinogenic amino acid
whose side group cyclizes onto the backbone: it
links to the α-amino group, and thus is also the
only proteinogenic amino acid containing a
secondary amine at this position. Proline has
sometimes been termed an imino acid, but this is
not correct by current nomenclature rules.
OVERVIEW cont.
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Over one hundred amino acids have been
found in nature. Some of these have been
detected in meteorites, especially in a type known
as carbonaceous chondrites.
Microorganisms and plants can produce
uncommon amino acids, which can be found in
peptidic antibiotics (e.g., nisin or alamethicin).
Lanthionine is a sulfide-bridged alanine dimer
which is found together with unsaturated amino
acids in lantibiotics (antibiotic peptides of
microbial origin).
Aminocyclopropane-1-carboxylic acid (ACC) is
a small disubstituted cyclic amino acid and a key
intermediate in the production of the plant
hormone ethylene.
OVERVIEW cont.
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In addition to protein synthesis, amino acids have
other biologically-important roles. Glycine and
glutamate are neurotransmitters as well as standard
amino acids in proteins. Many amino acids are used
to synthesize other molecules, for example:
Tryptophan is a precursor of the neurotransmitter
serotonin.
Glycine is one of the reactants in the synthesis of
porphyrins such as heme.
Arginine is used to synthesize the hormone nitric
oxide.
Numerous non-standard amino acids are also
biologically-important: Gamma-aminobutyric acid is
another neurotransmitter, carnitine is used in lipid
transport within a cell, ornithine, citrulline,
homocysteine, hydroxyproline, hydroxylysine, and
sarcosine.
OVERVIEW cont.
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Some of the 20 standard amino acids are called
essential amino acids because they cannot be
synthesized by the body from other compounds
through chemical reactions, but instead must be
taken in with food. In humans, the essential
amino acids are lysine, leucine, isoleucine,
methionine, phenylalanine, threonine, tryptophan,
valine. Histidine and arginine are generally
considered essential only in children, because of
their inability to synthesise them given their
undeveloped metabolisms.
The phrase "branched-chain amino acids" is
sometimes used to refer to the aliphatic amino
acids: leucine, isoleucine and valine.
GENERAL STRUCTURE
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The general structure of
proteinogenic alpha amino acids is:
R
|
H2N-----C----COOH
|
H
Structure cont.
Where R represents a side chain
specific to each amino acid. Amino
acids are usually classified by the
properties of the side chain into four
groups. The side chain can make
them behave like a weak acid, a
weak base, a hydrophile, if they are
polar, and hydrophobe if they are
nonpolar.
ISOMERISM
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Most amino acids occur in two possible optical
isomers, called D and L. The L amino acids
represent the vast majority of amino acids found
in proteins.
D amino acids are found in some proteins
produced by exotic sea-dwelling organisms, such
as cone snails. They are also abundant
components of the proteoglycan cell walls of
bacteria.
The D-isomer of aspartic acid is found in some
proteins as the result of a spontaneous posttranslational modification associated with protein
aging or as the by-product of enzymatic
modification catalyzed by protein L-isoaspartyl
methyltransferase.
Sterochemistry
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All amino acids (except glycine) recovered from
polypeptides are optically active and direction of angle
of rotation is measured by polarimeter.
Optically active molecules are asymmetric and the
central atoms (C-alpha atoms of amino acids) in such
molecules are chiral centers with property of
chirality.
These asymmetric centers give rise to enantiomers
(nonsuperimposable mirror images of one another) or
are stereoisomers (chiral molecules with different
configurations about at least one of their asymmetric
centers but which are otherwise identical).
Life is based on chiral molecules as biosynthetic
processes almost invariably produce pure
stereoisomers.
Isomerism cont.
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The L and D conventions for amino acid
do not refer to their own optical activity,
but rather to the optical activity of
glyceraldehyde as an analogue of the
amino acids.
In the RS system or Cahn-Ingold-Prelog,
S-glyceraldehyde is levorotary, and Rglyceraldehyde is dexterorotary, and so Samino acids are called "L-" even if they
are not levorotary, and R- amino acids are
likewise called "D-" even if they are not
dexterorotary.
Isomerism cont.
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Two exceptions exist:
In glycine, where R = H, and there is no
isomerism, because two groups on the
central carbon atom are identical
In cysteine, the L-S and D-R assignment
is reversed to L-R and D-S. Cysteine is
structured similarly (with respect to
glyceraldehyde) to the other amino acids
but the sulfur atom alters the
interpretation of the Cahn Ingold Prelog
rules.
PEPTIDE BONDING
Proteins are created by
polymerization of amino acids. This
condensation reaction yields the
newly formed peptide bond and a
molecule of water.
FORMATION OF PEPTIDE BONDING
Fig. 1 alpha amino acid
Fig. 2 zwitterion structure
Fig. 3 Two amino acids forming a peptide bond
ARBITRARY CLASSIFICATION OF THE 20
STANDARD AMINO ACIDS
Amino acids are classified by their polarities of their
side chains. There are 3 major type of amino acids:
I.
II.
III.
THE NON POLAR R GROUP
UNCHARGED POLAR SIDE CHAINS
CHARGED POLAR SIDE CHAINS
Non-polar, aliphatic, R groups – 9 acids :
Glycine (Gly/G)
Alanine (Ala/A)
Valine (Val/V)
Leucine (Leu/L
Isoleucine (Ile/I)
These have aliphatic hydrocarbon side chains ranging
in size from a methyl group for alanine to isomeric
butyl groups for L and I.
Non-polar R groups cont.
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Methionine (Met/M) – has thioether side
chain resembling n-butyl group in
physical properties.
Proline (Pro/P) – has a cyclic pyrrolidine
side group.
Phenylalanine (Phe/F) – has phenyl
moiety)- non-polar aromatic side group
Tryptophan (Trp/W) – has indole nonpolar aromatic side group
Non-polar amino acid side chains: Gly, Ala, Val, Leu, Ile,
Met, Pro, Phe, Trp
6 Amino acids with uncharged polar
side chains
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Serine and threonine bear hydroxylic R
groups of different sizes.
Asparagine and glutamine have amidebearing side chains of different sizes.
Tryosine has a phenolic group and is
aromatic.
Cysteine has a thiol group and can form a
disulfide bond with another cysteine.
Serine (Ser/S), Threonine (Thr/T), Asparagine (Asp/N),
Glutamine (Gln/Q), Tyrosine (Try/Y), Cysteine (Cys/C)
5 Amino acids with charged polar side
chains, + or 
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The side chains of basic amino acids are
positively charged at physiological pH
values:
Lysine – has butylammonium side chain
Arginine – bears a guanidino group
Histidine – carries a imidazolium moeity
The side chains of aspartic acid and
glutamic acid are negatively charged
above pH 3.
Amino acids with charged side chains:
Lysine (Lys/K), Arginine (Arg/R), Histidine (His/H), Aspartic acid
(Asp/D), & Glutamic acid (Glu/E)
AMINO ACID DERIVATIVES
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SIDE CHAIN MODIFICATIONS
The ‘universal’ genetic code specifies only the 20
essential amino acids.
Other amino acids are components of certain proteins
resulting from the specific modification of an amino
acid residue after the polypeptide chain has been
synthesized.
These modifications include the simple addition of
small chemical groups to certain amino acid chains:
hydroxylation, methylation, acetylation, and
phosphorylation.
Larger groups, including lipids and carbohydrate
polymers, are attached to particular amino acid
residues of certain proteins
Examples: o- phosphoserine, alpha-carboxyglutamate,
4-hydroxyprolone, 3-methyhistidine
BIOLOGICALLY ACTIVE AMINO ACIDS
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The 20 standard amino acids undergo a bewildering
number of chemical transformations to other amino
acids and related compounds as part of their normal
cellular synthesis and degradation.
Many organisms use certain amino acids to transport
nitrogen in the form of amino groups.
Amino acids may also be oxidized as metabolic fuels
to provide energy.
Amino acids often function as chemical messengers
for communication between cells.
Alpha-aminobutric acid and dopamine are neuro
transmitters.
Histamine is a mediator of allergic reactions.
Thyroxine stimulates vertebrate metabolism.
Many peptides (e.g. glutathione) have physiological
functions as hormones or regulatory molecules.